Calculating Strand Bias

[Jon17]

I'm doing sequence capture. How do I determine the average strand bias? When I look at the vcf files all the numbers are negative so I'm not sure that's correct. And although I can create a snp and cpg summary file with BisSNP as well as vcf files but I'm not sure how to interpret the output. When I awk out all the SB numbers in a vcf file they are many large numbers and all arenegative. So I'm not sure how people are getting small positive numbers for average strand bias. Any help is appreciated.

Thanks,


Filter SNP/methylation calls
java -Xmx10g -jar /path/to/BisSNP-0.82.2.jar -R ref.fa -T VCFpostprocess -oldVcf SAMPLE.snp.raw.sorted.vcf -newVcf SAMPLE.snp.filtered.vcf -snpVcf SAMPLE.snp.raw.sorted.vcf -o SAMPLE.snp.filter.summary.txt
java -Xmx10g -jar /path/to/BisSNP-0.82.2.jar -R ref.fa -T VCFpostprocess -oldVcf SAMPLE.cpg.raw.sorted.vcf -newVcf SAMPLE.cpg.filtered.vcf -snpVcf SAMPLE.snp.raw.sorted.vcf -o SAMPLE.cpg.filter.summary.txt


Convert VCF to BED file
perl /path/to/vcf2bed6plus2.strand.pl SAMPLE.snp.filtered.vcf
perl /path/to/vcf2bed6plus2.strand.pl SAMPLE.cpg.filtered.vcf